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- PDB-7l04: Crystal Structure of Adeno-Associated Virus Porcine Origin capsid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l04 | |||||||||
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Title | Crystal Structure of Adeno-Associated Virus Porcine Origin capsid protein in complex with Importin-alpha 2 | |||||||||
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![]() | TRANSPORT PROTEIN / Complex / transport / Nuclear Localization | |||||||||
Function / homology | ![]() Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / T=1 icosahedral viral capsid / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / T=1 icosahedral viral capsid / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / structural molecule activity / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hoad, M. / Forwood, J. | |||||||||
![]() | ![]() Title: Crystal Structure of Adeno-Associated Virus Porcine Origin capsid protein in complex with Importin-alpha 2 Authors: Hoad, M. / Forwood, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.5 KB | Display | ![]() |
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PDB format | ![]() | 134.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.7 KB | Display | ![]() |
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Full document | ![]() | 433.8 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bw0S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 1265.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 55268.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.6M Na citrate, 0.01M DTT, 0.1M HEPES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→44.67 Å / Num. obs: 33929 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 34.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.26→2.33 Å / Rmerge(I) obs: 0.888 / Num. unique obs: 3034 / CC1/2: 0.759 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6bw0 Resolution: 2.26→44.67 Å / SU ML: 0.278 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3607 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→44.67 Å
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Refine LS restraints |
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LS refinement shell |
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